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A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility

Nature Cell Biology volume 12, pages 1014–1020 (2010)Cite this article

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Abstract

Key regulators of 3′ untranslated regions (3′ UTRs) are microRNAs and RNA-binding proteins (RBPs)1,2. The p27 tumour suppressor is highly expressed in quiescent cells, and its downregulation is required for cell cycle entry after growth factor stimulation3,4. Intriguingly, p27 accumulates in quiescent cells despite high levels of its inhibitors miR-221 and miR-222 (Refs 5, 6). Here we show that miR-221 and miR-222 are underactive towards p27-3′ UTR in quiescent cells, as a result of target site hindrance. Pumilio-1 (PUM1) is a ubiquitously expressed RBP that was shown to interact with p27-3′ UTR7,8. In response to growth factor stimulation, PUM1 is upregulated and phosphorylated for optimal induction of its RNA-binding activity towards the p27-3′ UTR. PUM1 binding induces a local change in RNA structure that favours association with miR-221 and miR-222, efficient suppression of p27 expression, and rapid entry to the cell cycle. We have therefore uncovered a novel RBP-induced structural switch modulating microRNA-mediated gene expression regulation.

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Figure 1: miR-221 and miR-222 are underactive towards p27 in quiescent cells.
Figure 2: Pumilio is required for miR-221 and miR-222 function.
Figure 3: PUM1 RNA-binding activity is enhanced in cycling versus quiescent cells.
Figure 4: Pumilio regulates p27-dependent cell cycle re-entry from quiescence.
Figure 5: Pumilio binding alters local p27-3′ UTR structure and miR-221 and miR-222 accessibility.

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Acknowledgements

We thank all members of the Agami laboratory for technical help and discussions. We also thank André Gerber for constructs, Kees Jalink for advice on fluorescence lifetime imaging microscopy measurements, and R. B. Israel for assistance with statistical analysis. This work was supported by the EURYI (European research young investigator award), ERC (European Research Council), KWF (koningin wilhelmina fonds; Dutch cancer foundation) and Horizon-NWO (Nederlandse Organisatie voor Wetenschappelijk Onderzoek; R.A.) and an EMBO long-term fellowship (R.E.).

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  1. Martijn Kedde and Marieke van Kouwenhove: These authors contributed equally to this work

Authors and Affiliations

  1. Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands

    Martijn Kedde, Marieke van Kouwenhove, Joachim A. F. Oude Vrielink, Ran Elkon & Reuven Agami

  2. Division of Cell Biology II, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands

    Wilbert Zwart

  3. Centre for Biomedical Genetics UMCU, Stratenum 3.223, Universiteitsweg 100, 3584, CG Utrecht, The Netherlands

    Reuven Agami

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  1. Martijn Kedde
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Contributions

M.K. and M.v.K. performed most of the experimental work. R.A. supervised the project. W.Z. performed fluorescence lifetime imaging microscopy and confocal laser scanning microscopy analyses. J.O.V. provided technical assistance. R.E. performed bioinformatical analyses. M.K., M.v.K. and R.A. wrote the manuscript.

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Correspondence to Reuven Agami.

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Kedde, M., van Kouwenhove, M., Zwart, W. et al. A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol 12, 1014–1020 (2010). https://doi.org/10.1038/ncb2105

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